Abstract 5933: Trimodal molecular analysis in single cells of a primary breast cancer cohort with ResolveOME ™ amplification
Authors: Jon S. Zawistowski, Isai Salas-Gonzalez, Tia A. Tate, Tatiana V. Morozova, Katherine Kennedy, Durga M. Arvapalli, Swetha D. Velivela, Jamie E. Remington, Josh Croteau, Kevin Taylor, Jeff G. Blackinton, Victor J. Weigman, Jeffrey R. Marks, Eun-Sil Shelley Hwang, Gary L. Harton, Jay A. West
Journal: Cancer Research (2023)

Abstract The ResolveOME™ single-cell amplification solution unites whole-genome and full-length transcriptome information from the same cell, providing critical insight between these layers not possible when analyzed in isolation. We expand here upon the core layers of ResolveOME™ with the incorporation of BioLegend TotalSeq™ antibody oligo conjugates to investigate the expression of a panel of extracellular proteins in conjunction with the genomic and transcriptomic data. The present study demonstrates the power of exploring all tiers of the Central Dogma of Biology in a series of experiments aimed at defining the molecular characteristics facilitating the transition from Ductal Carcinoma In Situ (DCIS) to Invasive Ductal Carcinoma (IDC), sequencing single cells from mastectomy samples from twelve patients in collaboration with Duke University Medical Center. We either enriched for ductal epithelial cells by fluorescence-activated cell sorting (FACS) or dispensed single cells agnostic to marker and relied on the full transcriptome output of ResolveOME™ to report cell identity. At the genomic level, we identified oncogenic driver mutations in PIK3CA (H1047R, N345K) and distinct classes of copy number loss at either or both Chr. 13 and 16q/17p, harboring BRCA2/RB1 and TP53 tumor suppressor loci—whereby both SNV and CNV both varied in frequency within single cells of each patient and between patients of the cohort. These oncogenic mutations were nearly exclusive to biopsy cells of epithelial identity. However, intriguingly, ResolveOME™ uncovered cells of stem-like identity harboring PIK3CA missense mutations as well as uncovered cells still formally identified as epithelial and harboring mutant PIK3CA but with differential expression profiles—indicative of cells morphing cell state. Finally, the TotalSeq™ antibody panel unveiled intercellular heterogeneity and interpatient heterogeneity both in cell-surface protein phenotype of immune cells and in epithelial identity and signaling. This ongoing study continues to catalog the three omic layers in increasing numbers of single cells and significantly expanding targeted surface-protein analysis harnessing the power of the single-cell united data to determine the “penetrance” of genomic changes in the context of cognate transcript and protein information, with the ultimate goals of defining DCIS to IDC transition factors as well as novel biomarker identification that may be exploited therapeutically. Citation Format: Jon S. Zawistowski, Isai Salas-Gonzalez, Tia A. Tate, Tatiana V. Morozova, Katherine Kennedy, Durga M. Arvapalli, Swetha D. Velivela, Jamie E. Remington, Josh Croteau, Kevin Taylor, Jeff G. Blackinton, Victor J. Weigman, Jeffrey R. Marks, Eun-Sil Shelley Hwang, Gary L. Harton, Jay A. West. Trimodal molecular analysis in single cells of a primary breast cancer cohort with ResolveOME ™ amplification. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5933.